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Immortalin / peptide-shaker

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Parsing protein descriptions #4

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

1. Running of any omx etc.. other than the test files provided by peptide 
shaker which function correctly. Omx files are created using SearchGUI and the 
omx file outputted is operable in omssa-Parser's Omssa Viewer. 
2.
3.

What is the expected output? What do you see instead?

Results after completion of Data import progress. Instead error message says 
Display problem: A problem occurred while displaying results. Please send the 
log file to the developers.
Having looked in the conf file I cannot identify a peptideshaker.log file.

What version of the product are you using? On what operating system?

I'm using peptide shaker 0.9.3 run on windows 7 32bit with java version 6 
update 26 installed.

Please provide any additional information below.

The test files run fine and results are displayed. Samples i run myself through 
searchGUI using a mgf created in DataAnalysis and a FASTA downloaded from 
Uniprot does not work. 

This software looks great and would be really useful. I'm sure its a simple 
fault with what I'm doing but can't identify what.
Thank you in advance for any assistance.

Joseph Longworth 
j.longworth@shef.ac.uk

Original issue reported on code.google.com by josephlo...@gmail.com on 4 Oct 2011 at 1:31

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GoogleCodeExporter commented 9 years ago 
Thank you for your report. It can be that windows does not display the 
extension of PeptideShaker.log. If you look in the conf file there should be a 
text file named PeptideShaker. Would be of greatest help if you could provide 
it.
Also, if you could attach the omx file we will try to locate the bug.

Original comment by mvau...@gmail.com on 4 Oct 2011 at 2:04

GoogleCodeExporter commented 9 years ago 
Hi 

Have attached the log file and a compressed version of the .omx as it was above 
the 10mb attachment limit. If you want it uncompressed then could try to send 
it you in some other way.

Thanks again for the help
Joseph

Original comment by josephlo...@gmail.com on 4 Oct 2011 at 3:14

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GoogleCodeExporter commented 9 years ago 
Sorry for the late reply.

There seems to be a problem with the parsing of the description of your 
proteins. We are currently working a on a new version of PeptideShaker that we 
hope will solve the issue with your files as well.

Could you send us the the mgf file you are using?

We will then test your files in the new version and make any changes if needed.

The new version will be released next week. (We hope...)

Original comment by harald.b...@gmail.com on 9 Oct 2011 at 7:28

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 9 Oct 2011 at 7:29

GoogleCodeExporter commented 9 years ago 
And which FASTA file are you using? The omx files seems to contain lots of 
proteins from the organism 'Chlamydomonas reinhardtii'. Is this the organism 
you are studying? 

I see that there's not a lot of proteins for this in UniProtKB/Swiss-Prot (270) 
but a lot more in UniProtKB/Swiss-Prot (14,858). So are you searching in a 
combined FASTA file for the two databases? Or in just one of them?

In any case it is of course vital that the same database is used both when 
searching using SearchGUI and later in PeptideShaker.

If I search your omx files using the combined FASTA file 
(http://www.uniprot.org/uniprot/?query=Chlamydomonas+reinhardtii&sort=score&form
at=*) the file is opened in PeptideShaker without the issues you describe 
above. Both in the new and the old version of PeptideShaker.

(Note: The FASTA file at the above link has to be made in to a target-decoy 
database using SearchGUI before being used in PeptideShaker.)

Original comment by harald.b...@gmail.com on 9 Oct 2011 at 8:25

GoogleCodeExporter commented 9 years ago 
Hi 
Yes the species i am working on is Chlamydomonas reinhardtii. I use the 
combined database from UniprotKB of ~15000 proteins which typically works for 
me while using it in Phenyx identifying 181 proteins 1102 peptides with the mgf 
used here. I have also tried using a FASTA from NCBI refseq and the same 
display problem occurred. 
I have attached my mgf created in DataAnalysis.

I have run this through SearchGUI-1.6.1 which i also use to create the reverse 
database. When i ran peptide-shaker i input the omx file that SearchGUI 
outputted and peptide shaker reported picking up the relevant mgf and fasta. I 
have attached my fasta  file in a separate comment due to the limit on 
attachment. 
I hope that my problems will be resolved in your update as this software looks 
great.

Thanks again for the help
Joseph

Original comment by josephlo...@gmail.com on 10 Oct 2011 at 7:03

Attachments:

GoogleCodeExporter commented 9 years ago 
FASTA

Original comment by josephlo...@gmail.com on 10 Oct 2011 at 7:04

Attachments:

GoogleCodeExporter commented 9 years ago 
Found and solved the problem! :)

It was not related to the parsing of the proteins as I thought at first, but 
rather to the parsing of your mgf file. We use the spectrum titles in our map 
of the mgf file for fast access to a given spectrum, and your spectrum titles 
contained an extra white space after the TITLE tag, e.g., "TITLE= Cmpd 1, 
+MSn(595.518188), 13.8 min". This confused our map and resulted in the issues.

It has been fixed in the new (soon to be released) version and I'm now able to 
parse all your files without issues.

I'll let you know when the new version has been released so that you can test 
it yourself.

Original comment by harald.b...@gmail.com on 10 Oct 2011 at 9:13

GoogleCodeExporter commented 9 years ago 
PeptideShaker v0.10.0 has just been released. This should fix your problem. If 
not please let us know.

Original comment by harald.b...@gmail.com on 19 Oct 2011 at 3:27